Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010981.1 Kokia drynarioides strain JFW-HI SEQ_125951, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 467599
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 158 characters in sequence are not A, C, G, or T
Found at i:1679 original size:29 final size:33
Alignment explanation
Indices: 1626--1694 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 33
1616 TCAACCCGAA
*
1626 TATATTATGTTATAAAAATTAATTATATTTA-T
1 TATATTATGTTATAAAAATTAATTATATGTATT
*
1658 TATATT-TGTTA-AATAA-TAATTATATGTATT
1 TATATTATGTTATAAAAATTAATTATATGTATT
1688 TATATTA
1 TATATTA
1695 AATCACTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 11 0.33
30 11 0.33
31 5 0.15
32 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (33 bp):
TATATTATGTTATAAAAATTAATTATATGTATT
Found at i:9181 original size:16 final size:16
Alignment explanation
Indices: 9160--9190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9150 CGATATTTAG
*
9160 TAATTACATTGAATAA
1 TAATTACATTCAATAA
9176 TAATTACATTCAATA
1 TAATTACATTCAATA
9191 TTAAGAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATTACATTCAATAA
Found at i:9267 original size:27 final size:27
Alignment explanation
Indices: 9237--9292 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
9227 TAATTATGTT
9237 AAATATATACAAT-T-TTTGTAAAATTTA
1 AAATATATA-AATCTATTT-TAAAATTTA
*
9264 AAATCTATAAATCTATTTTAAAATTTA
1 AAATATATAAATCTATTTTAAAATTTA
9291 AA
1 AA
9293 TTCGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 20 0.77
28 3 0.12
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
AAATATATAAATCTATTTTAAAATTTA
Found at i:10270 original size:16 final size:16
Alignment explanation
Indices: 10209--10273 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
10199 GATAATAAAT
*
10209 TTAATTATTATTAGATTA
1 TTAATTAATA-TA-ATTA
* *
10227 GTAATTTAATATAAATA
1 TTAA-TTAATATAATTA
*
10244 TGAA-TATATATAATTA
1 TTAATTA-ATATAATTA
10260 TTAATTAATATAAT
1 TTAATTAATATAAT
10274 ATTTTTATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
15 2 0.05
16 18 0.49
17 7 0.19
18 5 0.14
19 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (16 bp):
TTAATTAATATAATTA
Found at i:14096 original size:21 final size:21
Alignment explanation
Indices: 14066--14109 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
14056 TGGAATAAGA
*
14066 AATAAATCAAATT-ATTAGTTG
1 AATAAATC-AATTAATCAGTTG
*
14087 AATAAGTCAATTAATCAGTTG
1 AATAAATCAATTAATCAGTTG
14108 AA
1 AA
14110 GTGAATCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
AATAAATCAATTAATCAGTTG
Found at i:14586 original size:3 final size:3
Alignment explanation
Indices: 14578--14605 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14568 CCTTTGCTTC
14578 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
14606 ATGTTGGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:19848 original size:23 final size:24
Alignment explanation
Indices: 19817--19869 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
19807 TTAAAAAACT
*
19817 TGTTTATAAACAT-TAGATT-AACA
1 TGTTCATAAACATATA-ATTGAACA
19840 TGTTCATAAACATATAATTGAACA
1 TGTTCATAAACATATAATTGAACA
19864 TGTTCA
1 TGTTCA
19870 CAAATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
TGTTCATAAACATATAATTGAACA
Found at i:20408 original size:20 final size:21
Alignment explanation
Indices: 20374--20412 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20364 CCTTGCCCCC
*
20374 AAAAGAAAATTGAAAAAAATG
1 AAAAGAAAATGGAAAAAAATG
20395 AAAAG-AAATGGAAAAAAA
1 AAAAGAAAATGGAAAAAAA
20413 GAAGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (21 bp):
AAAAGAAAATGGAAAAAAATG
Found at i:20422 original size:19 final size:19
Alignment explanation
Indices: 20376--20422 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
20366 TTGCCCCCAA
*
20376 AAGAAAATTGAAAAAAATG
1 AAGAAAATGGAAAAAAATG
*
20395 AAAAGAAATGGAAAAAAA-G
1 AAGA-AAATGGAAAAAAATG
20414 AAGGAAAAT
1 AA-GAAAAT
20423 ACCCTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (19 bp):
AAGAAAATGGAAAAAAATG
Found at i:40895 original size:29 final size:30
Alignment explanation
Indices: 40841--40901 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
40831 ATAATTTACA
* *
40841 AAAATTAGACCAAATCAAAATTTCATGTAT
1 AAAATTACACAAAATCAAAATTTCATGTAT
40871 AAAATTACACAAAATCAAAA-TTCATGTAT
1 AAAATTACACAAAATCAAAATTTCATGTAT
40900 AA
1 AA
40902 TTTTAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (30 bp):
AAAATTACACAAAATCAAAATTTCATGTAT
Found at i:46535 original size:31 final size:31
Alignment explanation
Indices: 46500--46577 Score: 156
Period size: 31 Copynumber: 2.5 Consensus size: 31
46490 GAGTTGCAAA
46500 TAATGAAACTCATCAACCAGTTTTATTGCAT
1 TAATGAAACTCATCAACCAGTTTTATTGCAT
46531 TAATGAAACTCATCAACCAGTTTTATTGCAT
1 TAATGAAACTCATCAACCAGTTTTATTGCAT
46562 TAATGAAACTCATCAA
1 TAATGAAACTCATCAA
46578 ATTACTTACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.33
Consensus pattern (31 bp):
TAATGAAACTCATCAACCAGTTTTATTGCAT
Found at i:58596 original size:23 final size:22
Alignment explanation
Indices: 58570--58614 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
58560 TTTAAGGTTG
* *
58570 GTTTTACACTTATAATTTATAGT
1 GTTTCACACTTACAA-TTATAGT
*
58593 GTTTCACATTTACAATTATAGT
1 GTTTCACACTTACAATTATAGT
58615 ATATTTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (22 bp):
GTTTCACACTTACAATTATAGT
Found at i:68863 original size:6 final size:7
Alignment explanation
Indices: 68841--68876 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
68831 AGCTTAAACC
68841 AAATAAAA
1 AAAT-AAA
68849 AAATAAA
1 AAATAAA
68856 AAATAAA
1 AAATAAA
68863 AAAT-AA
1 AAATAAA
68869 AAATAAA
1 AAATAAA
68876 A
1 A
68877 GAAAAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.22
7 17 0.63
8 4 0.15
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:68865 original size:14 final size:13
Alignment explanation
Indices: 68841--68876 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
68831 AGCTTAAACC
68841 AAATAAAAAAATAAA
1 AAAT-AAAAAAT-AA
68856 AAATAAAAAATAA
1 AAATAAAAAATAA
68869 AAATAAAA
1 AAATAAAA
68877 GAAAAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 7 0.33
15 4 0.19
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:72994 original size:22 final size:22
Alignment explanation
Indices: 72944--72987 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
72934 CTCAACAATA
72944 TTATCTCCAAAATGAGAACCTG
1 TTATCTCCAAAATGAGAACCTG
*
72966 TTATCTCCAAAGTGAGAACCTG
1 TTATCTCCAAAATGAGAACCTG
72988 CTTTCTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (22 bp):
TTATCTCCAAAATGAGAACCTG
Found at i:89244 original size:19 final size:21
Alignment explanation
Indices: 89205--89244 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
89195 TTATACGAGT
89205 AATTACAATTAACCATAATTA
1 AATTACAATTAACCATAATTA
*
89226 AATT-CAATT-ACCATCATTA
1 AATTACAATTAACCATAATTA
89245 CTTTCCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTACAATTAACCATAATTA
Found at i:91252 original size:31 final size:31
Alignment explanation
Indices: 91214--91278 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
91204 CTTGGAGGGG
91214 AAAATGGAAAGCATATTATTAGTTATGGTTC
1 AAAATGGAAAGCATATTATTAGTTATGGTTC
*
91245 AAAATGGAAAGCATATTATTTGTTATGGTTC
1 AAAATGGAAAGCATATTATTAGTTATGGTTC
91276 AAA
1 AAA
91279 TGATGGGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (31 bp):
AAAATGGAAAGCATATTATTAGTTATGGTTC
Found at i:98048 original size:2 final size:2
Alignment explanation
Indices: 98043--98071 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
98033 TGTGTGTGTG
98043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
98072 GGTTGGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100840 original size:2 final size:2
Alignment explanation
Indices: 100833--100861 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
100823 GATTTATGCT
100833 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
100862 TTTGCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:108975 original size:24 final size:24
Alignment explanation
Indices: 108938--108984 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
108928 TTTAAGAGCT
*
108938 TGAGATTAAGATATATAT-TTTTA
1 TGAGATTAAAATATATATATTTTA
108961 TGAGAGTTAAAATATATATATTTT
1 TGAGA-TTAAAATATATATATTTT
108985 TTCATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (24 bp):
TGAGATTAAAATATATATATTTTA
Found at i:109077 original size:24 final size:24
Alignment explanation
Indices: 109028--109090 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
109018 AGAATAATTA
*
109028 AATTAAAATTTATCATTTTTTGATTT
1 AATTATAATTT-T-ATTTTTTGATTT
109054 AATTATAATTTTATTTATTT-ATTT
1 AATTATAATTTTATTT-TTTGATTT
*
109078 ATTTATAATTTTA
1 AATTATAATTTTA
109091 AAAGTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 20 0.59
25 4 0.12
26 10 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
AATTATAATTTTATTTTTTGATTT
Found at i:109090 original size:20 final size:19
Alignment explanation
Indices: 109035--109079 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
109025 TTAAATTAAA
*
109035 ATTTATCATTTTTTGATTT
1 ATTTATAATTTTTTGATTT
* *
109054 AATTATAATTTTATTTATTT
1 ATTTATAATTTT-TTGATTT
109074 ATTTAT
1 ATTTAT
109080 TTATAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATAATTTTTTGATTT
Found at i:111424 original size:23 final size:23
Alignment explanation
Indices: 111395--111445 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
111385 TGAATTTTTA
*
111395 TATAAATTTAT-TAAA-ATTTAAT
1 TATAAAATTATATAAATA-TTAAT
111417 TATAAAATTATATAAATATTAA-
1 TATAAAATTATATAAATATTAAT
111439 TATAAAA
1 TATAAAA
111446 ATAAACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 17 0.65
23 8 0.31
24 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAAAATTATATAAATATTAAT
Found at i:111940 original size:31 final size:30
Alignment explanation
Indices: 111902--111991 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 30
111892 TTTATTTTAA
*
111902 ATATATATAATTGAATCAAAATAAAAGTTTT
1 ATATATATAATTGAATCAAATTAAAA-TTTT
* * * *
111933 ATGTATATATTTGAACCATAATTAGAATTTT
1 ATATATATAATTGAATCA-AATTAAAATTTT
111964 ATATATATAATT-ACATCAAATTAAAATT
1 ATATATATAATTGA-ATCAAATTAAAATT
111992 ACACATTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
30 10 0.21
31 32 0.67
32 6 0.12
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (30 bp):
ATATATATAATTGAATCAAATTAAAATTTT
Found at i:118988 original size:21 final size:21
Alignment explanation
Indices: 118962--119033 Score: 56
Period size: 27 Copynumber: 3.1 Consensus size: 21
118952 TATTTTCACT
*
118962 ATTTTA-AATATAAAATATGTA
1 ATTTTATAATATAAAA-ATATA
*
118983 ATTTTATATTATAAAAATATA
1 ATTTTATAATATAAAAATATA
119004 ATTAATTATATATTAAATAAAAATATA
1 ATT--TTATA-A-T--ATAAAAATATA
119031 ATT
1 ATT
119034 CAATTTGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 13 0.32
22 8 0.20
23 5 0.12
25 1 0.02
27 14 0.34
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (21 bp):
ATTTTATAATATAAAAATATA
Found at i:119015 original size:25 final size:26
Alignment explanation
Indices: 118981--119038 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
118971 ATAAAATATG
*
118981 TAATTTTATATT-ATAAAAATATAAT
1 TAATTATATATTAATAAAAATATAAT
119006 TAATTATATATTAAATAAAAATATAAT
1 TAATTATATATT-AATAAAAATATAAT
119033 TCAATT
1 T-AATT
119039 TGGTTCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
27 14 0.48
28 4 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTATATATTAATAAAAATATAAT
Found at i:119032 original size:23 final size:24
Alignment explanation
Indices: 118965--119033 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
118955 TTTCACTATT
*
118965 TTAAATATAAAATATGTAATTTTATA
1 TTAAATA-AAAATAT-TAATTATATA
*
118991 TTATAA-AAATATAATTAATTATATA
1 TTA-AATAAAAAT-ATTAATTATATA
119016 TTAAATAAAAATA-TAATT
1 TTAAATAAAAATATTAATT
119034 CAATTTGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 5 0.14
24 3 0.08
25 21 0.57
26 6 0.16
27 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
TTAAATAAAAATATTAATTATATA
Found at i:122379 original size:47 final size:47
Alignment explanation
Indices: 122292--122381 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
122282 TGAATTGAAT
* * *
122292 TTTAATGCCGGTGTATTGTATCGTATTGGGCCTTAGGCCTAGCTGCC
1 TTTAATGCCGGTATATTGTATCGTATCGGGCATTAGGCCTAGCTGCC
* * *
122339 TTTAATGCTGGTATTTTGTA-CTGTATCGGGCATTATGCCTAGC
1 TTTAATGCCGGTATATTGTATC-GTATCGGGCATTAGGCCTAGC
122382 AGGCATCACG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 1 0.03
47 35 0.97
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (47 bp):
TTTAATGCCGGTATATTGTATCGTATCGGGCATTAGGCCTAGCTGCC
Found at i:123196 original size:16 final size:16
Alignment explanation
Indices: 123177--123211 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
123167 GGATGGGGAA
123177 GGAGTAAAAGTTTTAG
1 GGAGTAAAAGTTTTAG
*
123193 GGAGTAAAAGTTTTGG
1 GGAGTAAAAGTTTTAG
123209 GGA
1 GGA
123212 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (16 bp):
GGAGTAAAAGTTTTAG
Found at i:128259 original size:24 final size:24
Alignment explanation
Indices: 128205--128259 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
128195 AGTTTGCGAG
*
128205 TCGAAGTGATAAAATAAAATAAAA
1 TCGAAGAGATAAAATAAAATAAAA
*
128229 TCAAAGAGATAAAAT-AAATAAACA
1 TCGAAGAGATAAAATAAAATAAA-A
*
128253 TGGAAGA
1 TCGAAGA
128260 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.18
Consensus pattern (24 bp):
TCGAAGAGATAAAATAAAATAAAA
Found at i:133690 original size:47 final size:47
Alignment explanation
Indices: 133636--133725 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
133626 ATTGCTTCTG
* * *
133636 AAGTTAGTATGATTGCATAGGC-GTATTGATGGTAAATTTTGACTCTA
1 AAGTTAGTATGATAGCATA-GCTGCATTGATGGCAAATTTTGACTCTA
133683 AAGTTAGTATGATAGCATAGCTGCATTGATGGCAAATTTTGAC
1 AAGTTAGTATGATAGCATAGCTGCATTGATGGCAAATTTTGAC
133726 AGAAATTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 2 0.05
47 37 0.95
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (47 bp):
AAGTTAGTATGATAGCATAGCTGCATTGATGGCAAATTTTGACTCTA
Found at i:140234 original size:5 final size:5
Alignment explanation
Indices: 140224--140257 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
140214 AACAGTGTAA
*
140224 TATAT TATAT TATAT TATAT TAT-T TTTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
140258 AATTTATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:140255 original size:14 final size:14
Alignment explanation
Indices: 140224--140265 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
140214 AACAGTGTAA
140224 TATATTATATTATAT
1 TATATTAT-TTATAT
*
140239 TATATTATTTTTAT
1 TATATTATTTATAT
*
140253 TATATAATTTATA
1 TATATTATTTATA
140266 CCACATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATTATTTATAT
Found at i:141876 original size:34 final size:32
Alignment explanation
Indices: 141838--141903 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
141828 ATGTTTTTAT
*
141838 TTAAA-ATTAAATAAATTAATTTTTATATATTAAA
1 TTAAAGATAAAATAAA-TAATTTTT-T-TATTAAA
*
141872 TTAAAGATAAAATTAATAATTTTTTTATTAAA
1 TTAAAGATAAAATAAATAATTTTTTTATTAAA
141904 ATTTTCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.24
33 1 0.03
34 13 0.45
35 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
TTAAAGATAAAATAAATAATTTTTTTATTAAA
Found at i:142164 original size:31 final size:31
Alignment explanation
Indices: 142123--142182 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
142113 AATAATAAAT
*
142123 TTTTATTTTGAT-TTCTCTAAAAATGATAATA
1 TTTTAATTTGATCTT-TCTAAAAATGATAATA
* *
142154 TTTTAATTTGATCTTTTTAAAAATTATAA
1 TTTTAATTTGATCTTTCTAAAAATGATAA
142183 AGATATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (31 bp):
TTTTAATTTGATCTTTCTAAAAATGATAATA
Found at i:142810 original size:115 final size:115
Alignment explanation
Indices: 142646--142879 Score: 450
Period size: 115 Copynumber: 2.0 Consensus size: 115
142636 ACTGGATATA
*
142646 TGAGAGGAGGGTTCTAAAGAACAGTAATAGTTGAATATTTGTAATTTCTTATAAAATTTAGTTGT
1 TGAGAGGAGGGTTCTAAAGAACACTAATAGTTGAATATTTGTAATTTCTTATAAAATTTAGTTGT
*
142711 TAACAAAATAATTTTATTTATTATTTACATTAAATTTGAGTATTATTAAT
66 TAACAAAATAATTTTATTTATTATTTACATTAAATTTGAATATTATTAAT
142761 TGAGAGGAGGGTTCTAAAGAACACTAATAGTTGAATATTTGTAATTTCTTATAAAATTTAGTTGT
1 TGAGAGGAGGGTTCTAAAGAACACTAATAGTTGAATATTTGTAATTTCTTATAAAATTTAGTTGT
142826 TAACAAAATAATTTTATTTATTATTTACATTAAATTTGAATATTATTAAT
66 TAACAAAATAATTTTATTTATTATTTACATTAAATTTGAATATTATTAAT
142876 TGAG
1 TGAG
142880 TTAGAGTTGA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 117 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (115 bp):
TGAGAGGAGGGTTCTAAAGAACACTAATAGTTGAATATTTGTAATTTCTTATAAAATTTAGTTGT
TAACAAAATAATTTTATTTATTATTTACATTAAATTTGAATATTATTAAT
Found at i:147826 original size:15 final size:14
Alignment explanation
Indices: 147808--147854 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
147798 AGATGAAGAT
147808 GATGATGTGGACGAG
1 GATGATG-GGACGAG
147823 GATGA--GGACGAG
1 GATGATGGGACGAG
*
147835 GATGATGAGGATGAG
1 GATGATG-GGACGAG
147850 GATGA
1 GATGA
147855 AGATGCCGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 12 0.43
15 16 0.57
ACGTcount: A:0.32, C:0.04, G:0.47, T:0.17
Consensus pattern (14 bp):
GATGATGGGACGAG
Found at i:147829 original size:6 final size:6
Alignment explanation
Indices: 147787--147859 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
147777 AGAGATAGGA
* * * * * * *
147787 GATGAA GATGAA GATGAA GATGAT GATGTG GACGAG GATGAG GACGAG
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG
*
147835 GAT--- GATGAG GATGAG GATGAA GATG
1 GATGAG GATGAG GATGAG GATGAG GATG
147860 CCGACAACGA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
3 3 0.05
6 52 0.95
ACGTcount: A:0.37, C:0.03, G:0.42, T:0.18
Consensus pattern (6 bp):
GATGAG
Found at i:148685 original size:23 final size:22
Alignment explanation
Indices: 148637--148686 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
148627 TAGAGAACAT
* *
148637 ATATATTTTTTCACTAATATTT
1 ATATATTTTTTAACTAATATTA
148659 ATATATTTTTATAACTAAT-TTAA
1 ATATATTTTT-TAACTAATATT-A
148682 ATATA
1 ATATA
148687 AAGTAGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATATTTTTTAACTAATATTA
Found at i:154049 original size:31 final size:32
Alignment explanation
Indices: 154013--154075 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
154003 ACCCGAGTCA
* * * *
154013 TTTGAAAATTTTTATTAAACCT-TTCAAAATT
1 TTTGAAAATCTTAACTAAACCTCTTAAAAATT
154044 TTTGAAAATCTTAACTAAACCTCTTAAAAATT
1 TTTGAAAATCTTAACTAAACCTCTTAAAAATT
154076 CTCATTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTGAAAATCTTAACTAAACCTCTTAAAAATT
Found at i:154088 original size:21 final size:21
Alignment explanation
Indices: 154059--154099 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
154049 AAATCTTAAC
154059 TAAACCTCTTAAAAATTCTCAT
1 TAAACCTCTTAAAAA-TCTCAT
154081 TAAA-CTCTTAAAAATCTCA
1 TAAACCTCTTAAAAATCTCA
154100 CAAAAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAACCTCTTAAAAATCTCAT
Found at i:154106 original size:21 final size:21
Alignment explanation
Indices: 154064--154107 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
154054 TTAACTAAAC
**
154064 CTCTTAAAAATTCTCATTAAA
1 CTCTTAAAAATTCTCAAAAAA
154085 CTCTTAAAAA-TCTCACAAAAA
1 CTCTTAAAAATTCTCA-AAAAA
154106 CT
1 CT
154108 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (21 bp):
CTCTTAAAAATTCTCAAAAAA
Found at i:154116 original size:12 final size:12
Alignment explanation
Indices: 154101--154133 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
154091 AAAATCTCAC
*
154101 AAAAACTAAAAA
1 AAAAAATAAAAA
154113 AAAAAATAAAAA
1 AAAAAATAAAAA
154125 AAAAAATAA
1 AAAAAATAA
154134 GCTTTCTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAAATAAAAA
Found at i:162141 original size:25 final size:23
Alignment explanation
Indices: 162090--162189 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
162080 CACTAGCGCG
*
162090 CTCTCTGTTTAGCAC-GTCTCGTA
1 CTCTCTGTTTAGCACTGTGT-GTA
*
162113 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG-T-TTAGCACTGTGTGTA
** * *
162138 CTCTCTAATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTA
*
162161 CTCTCTGTTTAGCATTGTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTA
162184 CTCTCT
1 CTCTCT
162190 ATTGCCCAGC
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 43 0.69
24 1 0.02
25 15 0.24
26 3 0.05
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTA
Found at i:163251 original size:23 final size:23
Alignment explanation
Indices: 163224--163267 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
163214 ATAAGATATC
163224 TTCAT-TTTATTTTCTTAATATTT
1 TTCATATTTATTTTC-TAATATTT
*
163247 TTCATATTTGTTTTCTAATAT
1 TTCATATTTATTTTCTAATAT
163268 GTAGATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (23 bp):
TTCATATTTATTTTCTAATATTT
Found at i:164075 original size:22 final size:22
Alignment explanation
Indices: 164026--164068 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
164016 ATTTGAAAAA
*
164026 AAAAAAAAATACACATTGGACC
1 AAAAAAACATACACATTGGACC
164048 ATAAAAAACA-ACACATTGGAC
1 A-AAAAAACATACACATTGGAC
164069 TGAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (22 bp):
AAAAAAACATACACATTGGACC
Found at i:164080 original size:20 final size:22
Alignment explanation
Indices: 164029--164082 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
164019 TGAAAAAAAA
164029 AAAAAAT-ACACATTGGACCAT
1 AAAAAATAACACATTGGACCAT
*
164050 AAAAAACAACACATTGGA-C-T
1 AAAAAATAACACATTGGACCAT
*
164070 GAAAAATAACACA
1 AAAAAATAACACA
164083 AGCATATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.41
21 7 0.24
22 10 0.34
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAAAATAACACATTGGACCAT
Found at i:173362 original size:16 final size:17
Alignment explanation
Indices: 173324--173362 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
173314 CTTGAGTTTT
*
173324 AATCAATTTCAAATTTA
1 AATCAATTTCAAATTCA
173341 AATCAA-TTCAAATTCA
1 AATCAATTTCAAATTCA
*
173357 AGTCAA
1 AATCAA
173363 AATTAATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (17 bp):
AATCAATTTCAAATTCA
Found at i:178934 original size:17 final size:16
Alignment explanation
Indices: 178901--178931 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
178891 TTTAATAGCC
*
178901 ACATCTCAAAAATTTA
1 ACATCCCAAAAATTTA
178917 ACATCCCAAAAATTT
1 ACATCCCAAAAATTT
178932 TAATGAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (16 bp):
ACATCCCAAAAATTTA
Found at i:183178 original size:59 final size:59
Alignment explanation
Indices: 183111--183237 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 59
183101 TAGTAGTACC
* * * * *
183111 CAACTATTAGTATATTTC-TTGTAGGTCATCTAATTATGAAAAGTGACAAAATGGTCACT
1 CAACTATTAGTAAATTTCTTTGTA-GTCACCCAACTATGAAAAGTGACAAAATGGTCACA
* * * *
183170 CAACTATTATTAAATTTCTTTTTTAGTCACCCAACTATGAAAAGTTACAAAATGTTCACA
1 CAACTATTAGTAAATTTC-TTTGTAGTCACCCAACTATGAAAAGTGACAAAATGGTCACA
183230 CAACTATT
1 CAACTATT
183238 TAATTTTGTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 16 0.28
60 37 0.65
61 4 0.07
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (59 bp):
CAACTATTAGTAAATTTCTTTGTAGTCACCCAACTATGAAAAGTGACAAAATGGTCACA
Found at i:197893 original size:48 final size:48
Alignment explanation
Indices: 197821--197923 Score: 188
Period size: 48 Copynumber: 2.1 Consensus size: 48
197811 AAGAATATTA
197821 TCTTATATGGCACATGCAACGCCTACTTGCTCTTTTAAACTTTATAAT
1 TCTTATATGGCACATGCAACGCCTACTTGCTCTTTTAAACTTTATAAT
*
197869 TCTTATATGGCACATGCAAGGCCTACTTGCTCTTTTAAACTTTATAAT
1 TCTTATATGGCACATGCAACGCCTACTTGCTCTTTTAAACTTTATAAT
*
197917 TATTATA
1 TCTTATA
197924 CTACTTAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (48 bp):
TCTTATATGGCACATGCAACGCCTACTTGCTCTTTTAAACTTTATAAT
Found at i:233285 original size:2 final size:2
Alignment explanation
Indices: 233272--233314 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
233262 TCTAAAATAT
*
233272 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
233314 T
1 T
233315 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:233319 original size:2 final size:2
Alignment explanation
Indices: 233314--233349 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
233304 TCTCTCTCTC
233314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
233350 TAATATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:238157 original size:15 final size:15
Alignment explanation
Indices: 238134--238205 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
238124 TTTCTACTTT
238134 TATAATATATATTTA
1 TATAATATATATTTA
*
238149 TATATTATATAATTTA
1 TATAATATAT-ATTTA
* *
238165 TATAATATAAAATTA
1 TATAATATATATTTA
*
238180 TATAA-ATGAT-TATA
1 TATAATAT-ATATTTA
238194 TATAATACTATA
1 TATAATA-TATA
238206 ATGAAAAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 9 0.20
15 22 0.49
16 14 0.31
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
TATAATATATATTTA
Found at i:238196 original size:24 final size:24
Alignment explanation
Indices: 238152--238198 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
238142 ATATTTATAT
* *
238152 ATTATATAATTTATATAATATAAA
1 ATTATATAAATGATATAATATAAA
238176 ATTATATAAATGAT-TATATATAA
1 ATTATATAAATGATATA-ATATAA
238199 TACTATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTATATAAATGATATAATATAAA
Found at i:240878 original size:31 final size:31
Alignment explanation
Indices: 240820--240879 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
240810 AACAATTCAG
*
240820 ACTCTTTTGAAAAGATTGATGGTCAAATTCC
1 ACTCTTTTGAAAAGATTGATGGCCAAATTCC
* *
240851 ACTCTTTTTAAAAGCTTGA-GAGCCAAATT
1 ACTCTTTTGAAAAGATTGATG-GCCAAATT
240880 TAGCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (31 bp):
ACTCTTTTGAAAAGATTGATGGCCAAATTCC
Found at i:245346 original size:23 final size:23
Alignment explanation
Indices: 245304--245364 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
245294 GAAATTTATT
*
245304 TATAAATTT-TTAATTGATTAAAA
1 TATAAATTTATT-ATTTATTAAAA
**
245327 TATAAATTTATTATTTATTAATT
1 TATAAATTTATTATTTATTAAAA
*
245350 TATAAGTTTA-TATTT
1 TATAAATTTATTATTT
245365 TTGAATGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 5 0.15
23 26 0.79
24 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
TATAAATTTATTATTTATTAAAA
Found at i:256822 original size:176 final size:177
Alignment explanation
Indices: 256241--256822 Score: 727
Period size: 176 Copynumber: 3.3 Consensus size: 177
256231 ATTTGAAAAA
*
256241 GTATTTTCTATGTGTTTGAATTTAGAAATTGGGTCATTCTTTTGGCAGCTTTG-GGTACT-TCTT
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATT-TTTTGGCAGCTTTGAGGTACTCT-TT
* * * ** *
256304 AATTACCCACCATTACTTGGTGTTTGTTTTCTGAGAAAGTAGTCGGAAAAGTTGTTGAAAGTAAT
64 AATTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGT-GGGAATGTTGTAAAAATTAAT
* ** *
256369 AAGGTTTAATCAAAAT-TATACCAAGAATATTTGAAAAATAA--TTTACTTT
128 AAGGTTT-AT-AAAATATATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
* * * * *
256418 GTATTTTCTCTGTGTTTTAATTTAGAATTTGGGTCGTTTTTTGGCAGTTTTGTGGTACTCTTTAA
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
* * ** *
256483 TTACCCACCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGAGGGGAAT-TTGTGCAAATTAGTAA
66 TTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAG-TGGGAATGTTGTAAAAATTAATAA
* * * * *
256547 GGTTTATAAAATATTCTGCAAAGGGTATTTG--AAGAAGTGTTTGCTTT
130 GGTTTATAAAATA-TATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
*
256594 GTATTTTTTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
*
256659 TTACCCATCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAATGGTTG-AAAAATTAATAA
66 TTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAAT-GTTGTAAAAATTAATAA
*
256723 GGTTTATAAAATAATGTACAAAGGGTATTTGAAAAAAAATGTTTACTTT
130 GGTTTATAAAAT-ATATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
* *
256772 GTA-TTTCTATGTGTTTTAATTTATAAATTGGGTCATTTTTT-ACAGCTTTGA
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGA
256823 TATCGTACGT
Statistics
Matches: 351, Mismatches: 42, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
174 8 0.02
175 8 0.02
176 191 0.54
177 127 0.36
178 17 0.05
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (177 bp):
GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
TTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAATGTTGTAAAAATTAATAAG
GTTTATAAAATATATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
Found at i:262337 original size:2 final size:2
Alignment explanation
Indices: 262330--262355 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
262320 CGAACAGTAA
262330 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
262356 TTGATGAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262588 original size:16 final size:18
Alignment explanation
Indices: 262562--262595 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
262552 TAGATTAAAG
262562 AGACAAAAGTT-ATTACC
1 AGACAAAAGTTGATTACC
262579 AGAC-AAAGTTGATTACC
1 AGACAAAAGTTGATTACC
262596 TTATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (18 bp):
AGACAAAAGTTGATTACC
Found at i:265822 original size:22 final size:22
Alignment explanation
Indices: 265805--265845 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
265795 TTATTTACTT
*
265805 AAAA-AAATTTAAACATTTATA
1 AAAATAAATTGAAACATTTATA
265826 AAAATAAATTGAAAC-TTTAT
1 AAAATAAATTGAAACATTTAT
265846 TGATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATAAATTGAAACATTTATA
Found at i:273172 original size:21 final size:19
Alignment explanation
Indices: 273142--273192 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
273132 TAAAAAATGA
273142 TTTCTGAAAAATAAATTACT
1 TTTCTGAAAAATAAA-TACT
*
273162 TTTCTGTAAAATTAAATACT
1 TTTCTG-AAAAATAAATACT
*
273182 TTTTTGAAAAA
1 TTTCTGAAAAA
273193 GTTAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 15 0.56
21 8 0.30
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (19 bp):
TTTCTGAAAAATAAATACT
Found at i:273199 original size:20 final size:20
Alignment explanation
Indices: 273146--273205 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
273136 AAATGATTTC
*
273146 TGAAAAA-TAAATTACTTTTC
1 TGAAAAATTAAA-TACTTTTT
*
273166 TGTAAAATTAAATACTTTTT
1 TGAAAAATTAAATACTTTTT
273186 TGAAAAAGTT-AATA-TTTTT
1 TGAAAAA-TTAAATACTTTTT
273205 T
1 T
273206 TATGTTTGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 6 0.17
20 23 0.66
21 6 0.17
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (20 bp):
TGAAAAATTAAATACTTTTT
Found at i:276994 original size:29 final size:29
Alignment explanation
Indices: 276943--277075 Score: 77
Period size: 29 Copynumber: 4.8 Consensus size: 29
276933 ACAAAATAAT
* **
276943 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAATGACTAAAATATAACATTTCA
* *
276972 AACATAAATGACTAAAATATAACCTGATACA
1 AACATAAATGACTAAAATATAACAT--TTCA
* *
277003 AACA-AAA--A-T--AAT-T-A-TTTTAA
1 AACATAAATGACTAAAATATAACATTTCA
**
277023 TAACATAAATGACTAAAACGTAACATTTCA
1 -AACATAAATGACTAAAATATAACATTTCA
* *
277053 AACATAAATAATTAAAATATAAC
1 AACATAAATGACTAAAATATAAC
277076 CTGATACAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
20 2 0.03
21 4 0.05
22 4 0.05
23 1 0.01
24 2 0.03
25 4 0.05
27 3 0.04
28 2 0.03
29 41 0.53
30 7 0.09
31 7 0.09
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (29 bp):
AACATAAATGACTAAAATATAACATTTCA
Found at i:277074 original size:81 final size:81
Alignment explanation
Indices: 276939--277106 Score: 300
Period size: 81 Copynumber: 2.1 Consensus size: 81
276929 CGTAACAAAA
* *
276939 TAATAACATAAGTGACTAAAACGTAACATTTCAAACATAAATGACTAAAATATAACCTGATACAA
1 TAATAACATAAATGACTAAAACGTAACATTTCAAACATAAATAACTAAAATATAACCTGATACAA
277004 ACAAAAATAATTATTT
66 ACAAAAATAATTATTT
*
277020 TAATAACATAAATGACTAAAACGTAACATTTCAAACATAAATAATTAAAATATAACCTGATACAA
1 TAATAACATAAATGACTAAAACGTAACATTTCAAACATAAATAACTAAAATATAACCTGATACAA
277085 ACAAAAATAATTATTT
66 ACAAAAATAATTATTT
*
277101 TTATAA
1 TAATAA
277107 TTTACCTAAC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (81 bp):
TAATAACATAAATGACTAAAACGTAACATTTCAAACATAAATAACTAAAATATAACCTGATACAA
ACAAAAATAATTATTT
Found at i:290577 original size:16 final size:18
Alignment explanation
Indices: 290558--290590 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
290548 AATTTAAGCT
290558 CAAAA-TAATTC-AAAAC
1 CAAAATTAATTCTAAAAC
290574 CAAAATTAATTCTAAAA
1 CAAAATTAATTCTAAAA
290591 TAAATAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (18 bp):
CAAAATTAATTCTAAAAC
Found at i:297369 original size:2 final size:2
Alignment explanation
Indices: 297362--297395 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
297352 ATGCTTATTT
297362 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
297396 AATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:304423 original size:125 final size:125
Alignment explanation
Indices: 304201--304450 Score: 491
Period size: 125 Copynumber: 2.0 Consensus size: 125
304191 CTATTTTCTG
304201 TTGATGGCGTGTAAATTTTGATCTGAATCTAAAAATCAAATTTTATTAATGTGAATTTAATTATA
1 TTGATGGCGTGTAAATTTTGATCTGAATCTAAAAATCAAATTTTATTAATGTGAATTTAATTATA
304266 TTTTAAAATTTGATTGTAAAAGTTCAATCCTCGAAAAGATAACCTCAAATAAGTAAAATC
66 TTTTAAAATTTGATTGTAAAAGTTCAATCCTCGAAAAGATAACCTCAAATAAGTAAAATC
*
304326 TTGATGGTGTGTAAATTTTGATCTGAATCTAAAAATCAAATTTTATTAATGTGAATTTAATTATA
1 TTGATGGCGTGTAAATTTTGATCTGAATCTAAAAATCAAATTTTATTAATGTGAATTTAATTATA
304391 TTTTAAAATTTGATTGTAAAAGTTCAATCCTCGAAAAGATAACCTCAAATAAGTAAAATC
66 TTTTAAAATTTGATTGTAAAAGTTCAATCCTCGAAAAGATAACCTCAAATAAGTAAAATC
304451 CCTTCTAACT
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (125 bp):
TTGATGGCGTGTAAATTTTGATCTGAATCTAAAAATCAAATTTTATTAATGTGAATTTAATTATA
TTTTAAAATTTGATTGTAAAAGTTCAATCCTCGAAAAGATAACCTCAAATAAGTAAAATC
Found at i:312013 original size:16 final size:17
Alignment explanation
Indices: 311992--312024 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
311982 GAAATTTTAC
*
311992 CTTTAATAA-TTTAAAA
1 CTTTAAAAACTTTAAAA
312008 CTTTAAAAACTTTAAAA
1 CTTTAAAAACTTTAAAA
312025 AATCTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
CTTTAAAAACTTTAAAA
Found at i:313387 original size:74 final size:74
Alignment explanation
Indices: 313306--313455 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 74
313296 TCACGAGTTG
*
313306 GATTTGGGCCGTAATTTTTAAATTCCACAGGTACCCGACTTAGTTATCTATATTTATTTTTATTT
1 GATTTGGGCCGTAATTTTTAAATTCCACAGGTACCCGACTTAGTTATCTATATGTATTTTTATTT
313371 TATATTTTT
66 TATATTTTT
*
313380 GATTTGGGCCGTAATTTTTAAATTCCACGGGTACCCGACTTAGTTATCTATATGTATTTTTATTT
1 GATTTGGGCCGTAATTTTTAAATTCCACAGGTACCCGACTTAGTTATCTATATGTATTTTTATTT
313445 TATATTTTT
66 TATATTTTT
313454 GA
1 GA
313456 ATTATTTACA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (74 bp):
GATTTGGGCCGTAATTTTTAAATTCCACAGGTACCCGACTTAGTTATCTATATGTATTTTTATTT
TATATTTTT
Found at i:313916 original size:21 final size:21
Alignment explanation
Indices: 313881--313931 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
313871 GAATTATGTA
*
313881 ATTTAGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
313902 GTTTGGATTTTTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
313923 ATTTGGATT
1 ATTTGGATT
313932 ATGCTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:318868 original size:24 final size:25
Alignment explanation
Indices: 318841--318888 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
318831 TTAATGAGTT
* *
318841 AATATTAATTCAATCA-AATACATA
1 AATAATAATTAAATCATAATACATA
*
318865 AATAATAATTAAATTATAATACAT
1 AATAATAATTAAATCATAATACAT
318889 CCACAATGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
AATAATAATTAAATCATAATACATA
Found at i:326221 original size:17 final size:17
Alignment explanation
Indices: 326196--326230 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
326186 ATATATTTTA
* *
326196 TAATTTTTAAATAAATT
1 TAATATTTAAAAAAATT
326213 TAATATTTAAAAAAATT
1 TAATATTTAAAAAAATT
326230 T
1 T
326231 CATCCATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATTTAAAAAAATT
Found at i:335868 original size:30 final size:30
Alignment explanation
Indices: 335830--335918 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
335820 ACGAAAATAT
* *
335830 TAAAAAAATATTATTAAAA-AATTAGAAATGA
1 TAAAAAATTA-TATAAAAATAATTA-AAATGA
*
335861 TAGAAAATTATATAAAAATAATTAAAATGA
1 TAAAAAATTATATAAAAATAATTAAAATGA
* * * *
335891 TAAAAAAATCTATAAAAATTACTAAAAT
1 TAAAAAATTATATAAAAATAATTAAAAT
335919 AAGTTATGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 36 0.73
31 13 0.27
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (30 bp):
TAAAAAATTATATAAAAATAATTAAAATGA
Found at i:337234 original size:23 final size:22
Alignment explanation
Indices: 337186--337235 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
337176 AAAAGTAATT
*
337186 ATATACATTTAAAATAAAACATA
1 ATATACA-TTAAAATAAAACACA
337209 ATATACA-TAAAATAAAATCTACA
1 ATATACATTAAAATAAAA-C-ACA
337232 ATAT
1 ATAT
337236 TAAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 1 0.04
23 13 0.54
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (22 bp):
ATATACATTAAAATAAAACACA
Found at i:355184 original size:23 final size:22
Alignment explanation
Indices: 355158--355229 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
355148 TTAAACGAAC
*
355158 ATAAACGAAGCTTGTTTATAAAT
1 ATAAACGAAGCTT-TATATAAAT
* * * *
355181 ATAAATG-AGCTTTAAACAAAC
1 ATAAACGAAGCTTTATATAAAT
*
355202 ATAAACGAATCTTATATATAAAT
1 ATAAACGAAGCTT-TATATAAAT
355225 ATAAA
1 ATAAA
355230 TGAACTAAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 11 0.30
22 9 0.24
23 17 0.46
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (22 bp):
ATAAACGAAGCTTTATATAAAT
Found at i:355203 original size:44 final size:44
Alignment explanation
Indices: 355137--355242 Score: 144
Period size: 44 Copynumber: 2.5 Consensus size: 44
355127 CGATGGAACA
* * * *
355137 ATAAATGAATTTTAAACGAACATAAACGAAGCTTGTTTATAAAT
1 ATAAATGAACTTTAAACAAACATAAACGAAGCTTATATATAAAT
* *
355181 ATAAATGAGCTTTAAACAAACATAAACGAATCTTATATATAAAT
1 ATAAATGAACTTTAAACAAACATAAACGAAGCTTATATATAAAT
355225 ATAAATGAAC--TAAACAAA
1 ATAAATGAACTTTAAACAAA
355243 TTTTATTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 8 0.15
44 47 0.85
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (44 bp):
ATAAATGAACTTTAAACAAACATAAACGAAGCTTATATATAAAT
Found at i:355533 original size:11 final size:11
Alignment explanation
Indices: 355514--355549 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
355504 AACTTCTAGA
355514 ATATATATATT
1 ATATATATATT
*
355525 ATATGTATATT
1 ATATATATATT
355536 ATATATATAATT
1 ATATATAT-ATT
355548 AT
1 AT
355550 TGATTGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Found at i:360641 original size:2 final size:2
Alignment explanation
Indices: 360634--360671 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
360624 AAATATAACC
360634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360672 GGTTAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:363016 original size:32 final size:32
Alignment explanation
Indices: 362970--363030 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
362960 TATATGATAT
* *
362970 TAATATATAAATATAGCAAATTTTGTATAAGA
1 TAATATATAAATATAGCAAAATTTATATAAGA
** *
363002 TAATATATTGATATATCAAAATTTATATA
1 TAATATATAAATATAGCAAAATTTATATA
363031 GAATATACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (32 bp):
TAATATATAAATATAGCAAAATTTATATAAGA
Found at i:363725 original size:3 final size:3
Alignment explanation
Indices: 363717--363746 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
363707 CCTCACACTC
363717 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
363747 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:364216 original size:30 final size:30
Alignment explanation
Indices: 364182--364263 Score: 71
Period size: 30 Copynumber: 2.7 Consensus size: 30
364172 TATAAAATAA
364182 TTATTATATTATTAAAAAAATTTATT-TAAG
1 TTATTATATTATTAAAAAAATTT-TTGTAAG
* * **
364212 TTATTGA-ATTATT-CAATAATTTTTGTTTG
1 TTATT-ATATTATTAAAAAAATTTTTGTAAG
*
364241 TCATTTATATTATTAAAAAAATT
1 TTA-TTATATTATTAAAAAAATT
364264 ATAAAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
28 2 0.05
29 12 0.30
30 19 0.47
31 7 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATTATATTATTAAAAAAATTTTTGTAAG
Found at i:367369 original size:25 final size:25
Alignment explanation
Indices: 367326--367374 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
367316 TTTTTTTTAA
*
367326 AAAAAATACTAAAATTATATAATTT
1 AAAAAATACTAAAATTATAAAATTT
*
367351 AAAAAATACT-TAATATATAAAATT
1 AAAAAATACTAAAAT-TATAAAATT
367375 ATTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAAATACTAAAATTATAAAATTT
Found at i:367385 original size:18 final size:18
Alignment explanation
Indices: 367335--367387 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 18
367325 AAAAAAATAC
*
367335 TAAAATTATATAATT-TA
1 TAAAATTATTTAATTATA
* *
367352 -AAAAATACTTAA-TATA
1 TAAAATTATTTAATTATA
367368 TAAAATTATTTAATTATA
1 TAAAATTATTTAATTATA
367386 TA
1 TA
367388 TATATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.04
16 11 0.39
17 10 0.36
18 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATTATTTAATTATA
Found at i:367387 original size:2 final size:2
Alignment explanation
Indices: 367382--367410 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
367372 ATTATTTAAT
367382 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
367411 ATAATTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:368427 original size:14 final size:14
Alignment explanation
Indices: 368385--368428 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
368375 TTGACTACTT
368385 TTTTATTTAAATTA
1 TTTTATTTAAATTA
* *
368399 -TTAATTTAAGGTTA
1 TTTTATTTAA-ATTA
368413 TTTTATTTAAATTA
1 TTTTATTTAAATTA
368427 TT
1 TT
368429 AGAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
TTTTATTTAAATTA
Found at i:372185 original size:23 final size:23
Alignment explanation
Indices: 372151--372256 Score: 81
Period size: 23 Copynumber: 4.6 Consensus size: 23
372141 GAACGCTAGC
*
372151 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTATTGTTTCGCACTTTGT
**
372174 GTGCTTATTGTTTCGCACTTCAT
1 GTGCTTATTGTTTCGCACTTTGT
* * *
372197 GTGCTTACTGATTT-GCGCTATGT
1 GTGCTTATTG-TTTCGCACTTTGT
* * * * *
372220 GCGCCTACTAGATT-GCACTGTGT
1 GTGCTTA-TTGTTTCGCACTTTGT
372243 GTGCTTATTGTTTC
1 GTGCTTATTGTTTC
372257 CCCAGCACTT
Statistics
Matches: 61, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 4 0.07
23 53 0.87
24 4 0.07
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (23 bp):
GTGCTTATTGTTTCGCACTTTGT
Found at i:374768 original size:14 final size:13
Alignment explanation
Indices: 374751--374780 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
374741 AAGTTTCATA
374751 TAAAAATTAAAAAT
1 TAAAAATT-AAAAT
374765 TAAAAATTAAAAT
1 TAAAAATTAAAAT
374778 TAA
1 TAA
374781 TGGTAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:374769 original size:6 final size:7
Alignment explanation
Indices: 374751--374780 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
374741 AAGTTTCATA
374751 TAAAAAT
1 TAAAAAT
374758 TAAAAAT
1 TAAAAAT
374765 TAAAAAT
1 TAAAAAT
374772 T-AAAAT
1 TAAAAAT
374778 TAA
1 TAA
374781 TGGTAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAAAT
Found at i:386471 original size:43 final size:43
Alignment explanation
Indices: 386418--386514 Score: 176
Period size: 43 Copynumber: 2.3 Consensus size: 43
386408 ATGGGATTAA
*
386418 TTTTTTTAATTAAAGTTGAAGTTCATAATTGATCAATGGTTAT
1 TTTTTTTAATTAAAATTGAAGTTCATAATTGATCAATGGTTAT
*
386461 TTTTTTTAATTAAAATTGAAGTTCATAATTGGTCAATGGTTAT
1 TTTTTTTAATTAAAATTGAAGTTCATAATTGATCAATGGTTAT
386504 TTTTTTTAATT
1 TTTTTTTAATT
386515 TTTAATTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (43 bp):
TTTTTTTAATTAAAATTGAAGTTCATAATTGATCAATGGTTAT
Found at i:394296 original size:29 final size:29
Alignment explanation
Indices: 394241--394296 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
394231 AAATGTTACC
*
394241 TAAATTTTTAATTTATAAAATTTGAATTT
1 TAAATTTTTAATTTATAAAATTCGAATTT
394270 TAAATTTTT-ATTTA-AGAAATATCGAAT
1 TAAATTTTTAATTTATA-AAAT-TCGAAT
394297 ATTCCCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.04
28 9 0.38
29 14 0.58
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (29 bp):
TAAATTTTTAATTTATAAAATTCGAATTT
Found at i:396015 original size:4 final size:4
Alignment explanation
Indices: 396006--396042 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
395996 GGATAATACA
396006 TATC TATC TATC TA-- TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
396043 ATATATTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:399599 original size:29 final size:29
Alignment explanation
Indices: 399566--399624 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
399556 TATGTTTTGA
**
399566 ATTATTAAATTATTTTAAAGTTTTTATTT
1 ATTATTAAATTATTCGAAAGTTTTTATTT
* * *
399595 ATTATTGAGTTCTTCGAAAGTTTTTATTT
1 ATTATTAAATTATTCGAAAGTTTTTATTT
399624 A
1 A
399625 AATTGTTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (29 bp):
ATTATTAAATTATTCGAAAGTTTTTATTT
Found at i:419775 original size:2 final size:2
Alignment explanation
Indices: 419764--419795 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
419754 TTTATCTATC
419764 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
419796 GAAATGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:422154 original size:29 final size:26
Alignment explanation
Indices: 422088--422159 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
422078 CACGAATATT
422088 TTTCACAAATTTAAATGTATTTTTTAA
1 TTTCA-AAATTTAAATGTATTTTTTAA
* *
422115 TTTTAAGAATTTAATATTTTATTTTTTATA
1 TTTCAA-AATTTAA-A-TGTATTTTTTA-A
*
422145 TTTCAAAATTCAAAT
1 TTTCAAAATTTAAAT
422160 TCAATTGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.03
27 12 0.32
28 2 0.05
29 16 0.43
30 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (26 bp):
TTTCAAAATTTAAATGTATTTTTTAA
Found at i:426708 original size:6 final size:6
Alignment explanation
Indices: 426697--426731 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
426687 CAAAAGGGAA
426697 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
426732 AGAGAGGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:427814 original size:19 final size:20
Alignment explanation
Indices: 427778--427828 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
427768 TTACAAAAAA
* **
427778 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAATAATTTAC
427798 AAAAATTCAAAAT-ATTTAC
1 AAAAATTCAAAATAATTTAC
427817 AAAAATTTCAAA
1 AAAAA-TTCAAA
427829 TTTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAC
Found at i:427884 original size:45 final size:44
Alignment explanation
Indices: 427793--427891 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 44
427783 ATCAAAATAA
* * *
427793 TTTTTAAAAATTCAAAATATTTACAAAAATTTCAAATTTTATAT
1 TTTTTAAAAATTCAAAAAATATACAAAAATTTCAAATTTTAAAT
* *
427837 TTTTTAAAAATTATAAAAAATATATAAAAA-TT-AAGATTTTAAAAT
1 TTTTTAAAAATT-CAAAAAATATACAAAAATTTCAA-ATTTT-AAAT
427882 TTTTCTAAAA
1 TTTT-TAAAA
427892 TAATTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
43 2 0.04
44 19 0.41
45 20 0.43
46 5 0.11
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (44 bp):
TTTTTAAAAATTCAAAAAATATACAAAAATTTCAAATTTTAAAT
Found at i:429796 original size:2 final size:2
Alignment explanation
Indices: 429789--429815 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
429779 GAACTCTCCT
429789 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
429816 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:454322 original size:16 final size:16
Alignment explanation
Indices: 454295--454333 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
454285 TAGCAAAACC
* *
454295 AAATGTTCCGAATTTG
1 AAATGATCCGAACTTG
*
454311 AATTGATCCGAACTTG
1 AAATGATCCGAACTTG
454327 AAATGAT
1 AAATGAT
454334 TAGAAAAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (16 bp):
AAATGATCCGAACTTG
Found at i:463307 original size:18 final size:16
Alignment explanation
Indices: 463275--463318 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
463265 ATAGAACGAG
463275 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
463291 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
463305 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
463319 ACTCTAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:463506 original size:11 final size:11
Alignment explanation
Indices: 463492--463527 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
463482 ATATCTAAAT
463492 AATAATAACAA
1 AATAATAACAA
*
463503 AATAGTAACAA
1 AATAATAACAA
*
463514 TATAATAACAA
1 AATAATAACAA
463525 AAT
1 AAT
463528 GATGGCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (11 bp):
AATAATAACAA
Found at i:465131 original size:6 final size:6
Alignment explanation
Indices: 465120--465153 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
465110 ATGGGAGATT
465120 AAAGCA AAAGCA AAAGCA AAAGCA AAAGCA AAAG
1 AAAGCA AAAGCA AAAGCA AAAGCA AAAGCA AAAG
465154 AGCGTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.15, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGCA
Done.